RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

Searching..................................................done

Query= 537021.9.peg.393_1
         (150 letters)



>gnl|CDD|58616 cd04250, AAK_NAGK-C, AAK_NAGK-C: N-Acetyl-L-glutamate kinase -
           cyclic (NAGK-C) catalyzes the phosphorylation of the
           gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in
           the second step of arginine biosynthesis found in some
           bacteria and photosynthetic organisms using the
           non-acetylated, cyclic route of ornithine biosynthesis.
           In this pathway, glutamate is first N-acetylated and
           then phosphorylated by NAGK to give phosphoryl NAG,
           which is converted to NAG-ornithine. There are two
           variants of this pathway. In one, typified by the
           pathway in Thermotoga maritima and Pseudomonas
           aeruginosa, the acetyl group is recycled by reversible
           transacetylation from acetylornithine to glutamate. The
           phosphorylation of NAG by NAGK is feedback inhibited by
           arginine. In photosynthetic organisms, NAGK is the
           target of the nitrogen-signaling protein PII. Hexameric
           formation of NAGK domains appears to be essential to
           both arginine inhibition and NAGK-PII complex formation.
           NAGK-C are members of the Amino Acid Kinase Superfamily
           (AAK)..
          Length = 279

 Score =  176 bits (447), Expect = 3e-45
 Identities = 66/130 (50%), Positives = 99/130 (76%)

Query: 12  ILEQVLPFVQFYENETIVVKYGGHVMNCTDLSKDFVNDIALLKKSNITPVIVHGGGPQIG 71
           +L + LP++Q +  +T+V+KYGG+ M   +L + F  DI LLK   I PV+VHGGGP+I 
Sbjct: 1   VLIEALPYIQKFRGKTVVIKYGGNAMKDEELKESFARDIVLLKYVGINPVVVHGGGPEIN 60

Query: 72  AVLEKMGIKSKFENGLRITDQQTAEVVEMVLAGSINKKIVSLINQTGTQAIGICGKDGNM 131
            +L+K+GI+S+F NGLR+TD++T E+VEMVL G +NK+IVSLIN+ G +A+G+ GKDGN+
Sbjct: 61  EMLKKLGIESEFVNGLRVTDEETMEIVEMVLVGKVNKEIVSLINRAGGKAVGLSGKDGNL 120

Query: 132 VFAEKARHSL 141
           + A+K   ++
Sbjct: 121 IKAKKKDATV 130


>gnl|CDD|58604 cd04238, AAK_NAGK-like, AAK_NAGK-like: N-Acetyl-L-glutamate kinase
           (NAGK)-like . Included in this CD are the Escherichia
           coli and Pseudomonas aeruginosa type NAGKs which
           catalyze the phosphorylation of N-acetyl-L-glutamate
           (NAG) by ATP in the second step of arginine biosynthesis
           found in bacteria and photosynthetic organisms using
           either the acetylated, noncyclic (NC), or
           non-acetylated, cyclic (C) route of ornithine
           biosynthesis. Also included in this CD is a distinct
           group of uncharacterized (UC) bacterial and archeal
           NAGKs. Members of this CD belong to the Amino Acid
           Kinase Superfamily (AAK)..
          Length = 256

 Score =  157 bits (399), Expect = 1e-39
 Identities = 60/109 (55%), Positives = 87/109 (79%)

Query: 28  IVVKYGGHVMNCTDLSKDFVNDIALLKKSNITPVIVHGGGPQIGAVLEKMGIKSKFENGL 87
           +V+KYGG  M   +L + F +DI LLK+  I PVIVHGGGP+I  +L+++GI+S+F NGL
Sbjct: 1   VVIKYGGSAMKDEELKEAFADDIVLLKQVGINPVIVHGGGPEINELLKRLGIESEFVNGL 60

Query: 88  RITDQQTAEVVEMVLAGSINKKIVSLINQTGTQAIGICGKDGNMVFAEK 136
           R+TD++T E+VEMVLAG +NK++VSL+N+ G +A+G+ GKDG ++ AEK
Sbjct: 61  RVTDKETMEIVEMVLAGKVNKELVSLLNRAGGKAVGLSGKDGGLIKAEK 109


>gnl|CDD|30894 COG0548, ArgB, Acetylglutamate kinase [Amino acid transport and
           metabolism].
          Length = 265

 Score =  150 bits (381), Expect = 1e-37
 Identities = 60/112 (53%), Positives = 83/112 (74%)

Query: 25  NETIVVKYGGHVMNCTDLSKDFVNDIALLKKSNITPVIVHGGGPQIGAVLEKMGIKSKFE 84
            +TIV+K GG  M   +L + F +DIALLK   I PV+VHGGGPQI  +L K+GI+ +F 
Sbjct: 2   GKTIVIKLGGSAMEDENLLEAFASDIALLKSVGIRPVVVHGGGPQIDEMLAKLGIEPEFV 61

Query: 85  NGLRITDQQTAEVVEMVLAGSINKKIVSLINQTGTQAIGICGKDGNMVFAEK 136
            GLR+TD +T EVVEMVL G++NK+IV+ +++ G QA+G+ G DGN+V A+K
Sbjct: 62  KGLRVTDAETLEVVEMVLGGTVNKEIVARLSKHGGQAVGLSGVDGNLVTAKK 113


>gnl|CDD|133644 CHL00202, argB, acetylglutamate kinase; Provisional.
          Length = 284

 Score =  138 bits (349), Expect = 7e-34
 Identities = 55/124 (44%), Positives = 81/124 (65%)

Query: 11  EILEQVLPFVQFYENETIVVKYGGHVMNCTDLSKDFVNDIALLKKSNITPVIVHGGGPQI 70
           ++L + LP++Q +    +V+KYGG  M    L  D + DI  L    +  V+VHGGGP+I
Sbjct: 9   QVLSEALPYIQKFRGRIMVIKYGGAAMKNLILKADIIKDILFLSCIGLKIVVVHGGGPEI 68

Query: 71  GAVLEKMGIKSKFENGLRITDQQTAEVVEMVLAGSINKKIVSLINQTGTQAIGICGKDGN 130
              L+++ I  KF NG+R+TD+ T E+VEMVLAG +NK +V  IN  G +A+G+CGKD N
Sbjct: 69  NFWLKQLNISPKFWNGIRVTDKVTMEIVEMVLAGKVNKDLVGSINANGGKAVGLCGKDAN 128

Query: 131 MVFA 134
           ++ A
Sbjct: 129 LIVA 132


>gnl|CDD|37647 KOG2436, KOG2436, KOG2436, Acetylglutamate kinase/acetylglutamate
           synthase [Amino acid transport and metabolism].
          Length = 520

 Score = 93.5 bits (232), Expect = 2e-20
 Identities = 33/123 (26%), Positives = 61/123 (49%), Gaps = 1/123 (0%)

Query: 11  EILEQVLPFVQFYENETIVVKYGGHVMNCTDLSKDFVNDIALLKKSNITPVIVHGGGPQI 70
            IL + LP++  + ++  VV   G  ++ T L     +D+A L    + P++V G  PQI
Sbjct: 80  RILRESLPYITSFRDQKFVVIKSGEAIS-TSLLHSLASDLAFLHHVGLRPIVVPGTQPQI 138

Query: 71  GAVLEKMGIKSKFENGLRITDQQTAEVVEMVLAGSINKKIVSLINQTGTQAIGICGKDGN 130
             +L + GI+ ++ +G R+TD  T +  +  ++   N  +V  ++Q GT+A         
Sbjct: 139 NRLLAERGIEPEYVDGYRVTDAHTLQAAKESVSLEANLNLVINLSQLGTRARPSSSGVRV 198

Query: 131 MVF 133
             F
Sbjct: 199 GNF 201


>gnl|CDD|144336 pfam00696, AA_kinase, Amino acid kinase family.  This family
           includes kinases that phosphorylate a variety of amino
           acid substrates, as well as uridylate kinase and
           carbamate kinase. This family includes: Aspartokinase
           EC:2.7.2.4. Acetylglutamate kinase EC:2.7.2.8. Glutamate
           5-kinase EC:2.7.2.11. Uridylate kinase EC:2.7.4.-.
           Carbamate kinase EC:2.7.2.2.
          Length = 230

 Score = 79.8 bits (197), Expect = 3e-16
 Identities = 36/118 (30%), Positives = 54/118 (45%), Gaps = 3/118 (2%)

Query: 26  ETIVVKYGGHVMNCTDLSKDFVNDIALLKKSNITPVIVHGGGPQIGAVLEKMGIKSKFEN 85
           + IV+K GG  +   D  K    +IALL +  I  V+V GGG     +L   GI  K   
Sbjct: 1   KRIVIKLGGSSLTDEDAIKRIAEEIALLSELGIKVVVVSGGGGFTDKLLAAYGIAEK--I 58

Query: 86  GLRITDQQTAEVVEMVLAGSINKKIVSLINQTGTQAIGICGKDGNMVFAEKARHSLRL 143
           GLR+T   T  ++E  LAG +   +VS   + G +A+ +   DG +       +    
Sbjct: 59  GLRVTAGATGLIIEAALAG-LLDIVVSAGERLGARAVALLLSDGGIGAVRLDANDTEA 115


>gnl|CDD|58615 cd04249, AAK_NAGK-NC, AAK_NAGK-NC: N-Acetyl-L-glutamate kinase -
           noncyclic (NAGK-NC) catalyzes the phosphorylation of the
           gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in
           the second step of microbial arginine biosynthesis using
           the acetylated, noncyclic route of ornithine
           biosynthesis. There are two variants of this pathway. In
           one, typified by the pathway in Escherichia coli,
           glutamate is acetylated by acetyl-CoA and
           acetylornithine is deacylated hydrolytically. In this
           pathway, feedback inhibition by arginine occurs at the
           initial acetylation of glutamate and not at the
           phosphorylation of NAG by NAGK. Homodimeric NAGK-NC are
           members of the Amino Acid Kinase Superfamily (AAK)..
          Length = 252

 Score = 71.5 bits (175), Expect = 9e-14
 Identities = 31/115 (26%), Positives = 61/115 (53%), Gaps = 1/115 (0%)

Query: 28  IVVKYGGHVMNCTDLSKDFVNDIA-LLKKSNITPVIVHGGGPQIGAVLEKMGIKSKFENG 86
           +V+K GG ++      +   + ++   ++ N   VIVHGGG  +  +L+K+   S+ +NG
Sbjct: 1   LVIKLGGALLETEAALEQLFSALSEYQQQHNRQLVIVHGGGCVVDELLKKLNFPSEKKNG 60

Query: 87  LRITDQQTAEVVEMVLAGSINKKIVSLINQTGTQAIGICGKDGNMVFAEKARHSL 141
           LR+T ++    +   LAG+ NK++++   + G + +G+   DG M    +    L
Sbjct: 61  LRVTPKEQIPYITGALAGTANKQLMAQAIKAGLKPVGLSLADGGMTAVTQLDPEL 115


>gnl|CDD|58618 cd04252, AAK_NAGK-fArgBP, AAK_NAGK-fArgBP: N-Acetyl-L-glutamate
           kinase (NAGK) of the fungal arginine-biosynthetic
           pathway (fArgBP). The nuclear-encoded, mitochondrial
           polyprotein precursor with an N-terminal NAGK (ArgB)
           domain (this CD), a central DUF619 domain, and a
           C-terminal reductase domain (ArgC, N-Acetylglutamate
           Phosphate Reductase, NAGPR). The precursor is cleaved in
           the mitochondria into two distinct enzymes (NAGK-DUF619
           and NAGPR). Native molecular weights of these proteins
           indicate that the kinase is an octamer whereas the
           reductase is a dimer. This CD also includes some
           gamma-proteobacteria (Xanthomonas and Xylella) NAG
           kinases with an N-terminal NAGK (ArgB) domain (this CD)
           and a C-terminal DUF619 domain. The DUF619 domain is
           described as a putative distant homolog of the
           acetyltransferase, ArgA, predicted to function in NAG
           synthase association in fungi. Eukaryotic sequences have
           an N-terminal mitochondrial transit peptide. Members of
           this NAG kinase domain CD belong to the Amino Acid
           Kinase Superfamily (AAK)..
          Length = 248

 Score = 69.5 bits (170), Expect = 3e-13
 Identities = 30/96 (31%), Positives = 52/96 (54%), Gaps = 3/96 (3%)

Query: 29  VVKYGGHVMNCTDLSKDFVNDIALLKKSNITPVIVHGGGPQIGAVLEKMGIKSKFENGLR 88
           V+K GG ++   D   +    ++ L+   + P++VHG GPQ+   LE  G++ ++ +GLR
Sbjct: 2   VIKVGGAII--EDDLDELAASLSFLQHVGLYPIVVHGAGPQLNEELEAAGVEPEYVDGLR 59

Query: 89  ITDQQTAEVVEMVLAGSINKKIVSLINQTGTQAIGI 124
           +TD +T  V   V     N K+V  + + G +A  I
Sbjct: 60  VTDPETLAVARKVFL-EENLKLVEALERNGARARPI 94


>gnl|CDD|58599 cd02115, AAK, Amino Acid Kinases (AAK) superfamily, catalytic
           domain; present in such enzymes like N-acetylglutamate
           kinase (NAGK), carbamate kinase (CK), aspartokinase
           (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK).
           The AAK superfamily includes kinases that phosphorylate
           a variety of amino acid substrates. These kinases
           catalyze the formation of phosphoric anhydrides,
           generally with a carboxylate, and use ATP as the source
           of the phosphoryl group; are involved in amino acid
           biosynthesis. Some of these kinases control the process
           via allosteric feed-back inhibition..
          Length = 248

 Score = 69.7 bits (170), Expect = 3e-13
 Identities = 29/103 (28%), Positives = 47/103 (45%), Gaps = 1/103 (0%)

Query: 29  VVKYGGHVMNCTDLSKDFVNDIALLKKSNITPVIVHGGGPQIGAVLEKMGIKSKFENGLR 88
           V+K+GG  ++  +  ++    +  L       V+VHG GPQI   L   G    +  GLR
Sbjct: 1   VIKFGGSSVSSEERLRNLARILVKLASEGGRVVVVHGAGPQITDELLAHGELLGYARGLR 60

Query: 89  ITDQQTAEVVEMVLAGSINKKIVSLINQTGTQAIGICGKDGNM 131
           ITD++T  +  M    S N  I + + Q G +A+ +       
Sbjct: 61  ITDRETDALAAMGEGMS-NLLIAAALEQHGIKAVPLDLTQAGF 102


>gnl|CDD|58603 cd04237, AAK_NAGS-ABP, AAK_NAGS-ABP: N-acetylglutamate (NAG)
           kinase-like domain of the NAG Synthase (NAGS) of the
           arginine-biosynthesis pathway (ABP) found in gamma- and
           beta-proteobacteria and higher plant chloroplasts.
           Domain architecture of these NAGS consisted of an
           N-terminal NAG kinase-like (ArgB) domain (this CD) and a
           C-terminal NAG synthase, acetyltransferase (ArgA)
           domain. Both bacterial and plant sequences in this CD
           have a conserved N-terminal extension; a similar
           sequence in the NAG kinases of the cyclic
           arginine-biosynthesis pathway has been implicated in
           feedback inhibition sensing. Plant sequences also have
           an N-terminal chloroplast transit peptide and an insert
           (approx. 70 residues) in the C-terminal region of ArgB.
           Members of this CD belong to the Amino Acid Kinase
           Superfamily (AAK)..
          Length = 280

 Score = 67.5 bits (165), Expect = 2e-12
 Identities = 33/102 (32%), Positives = 55/102 (53%), Gaps = 2/102 (1%)

Query: 15  QVLPFVQFYENETIVVKYGGHVMNCTDLSKDFVNDIALLKKSNITPVIVHGGGPQIGAVL 74
           +  P++  +  +T V+ +GG  +   +     V+DIALL    I  V+VHG  PQI   L
Sbjct: 8   EAAPYINAHRGKTFVIAFGGEAVAHPNFDN-IVHDIALLHSLGIRLVLVHGARPQIDQRL 66

Query: 75  EKMGIKSKFENGLRITDQQTAEVVEMVLAGSINKKIVSLINQ 116
            + G++ ++  GLRITD    E V    AG++  +I +L++ 
Sbjct: 67  AERGLEPRYHRGLRITDAAALECV-KEAAGAVRLEIEALLSM 107


>gnl|CDD|58617 cd04251, AAK_NAGK-UC, AAK_NAGK-UC: N-Acetyl-L-glutamate kinase -
           uncharacterized (NAGK-UC). This domain is similar to
           Escherichia coli and Pseudomonas aeruginosa NAGKs which
           catalyze the phosphorylation of the gamma-COOH group of
           N-acetyl-L-glutamate (NAG) by ATP in the second step of
           microbial arginine biosynthesis. These uncharacterized
           domain sequences are found in some bacteria (Deinococci
           and Chloroflexi) and archea and belong to the Amino Acid
           Kinase Superfamily (AAK)..
          Length = 257

 Score = 66.8 bits (163), Expect = 2e-12
 Identities = 43/127 (33%), Positives = 74/127 (58%), Gaps = 13/127 (10%)

Query: 28  IVVKYGGHVMNCTDLSKDFVNDIALLKKSNITPVIVHGGGPQIGAVLEKMGIKSKF---E 84
           IVVK GG V++      D    I  +       ++VHGGG  +   L+++G++ KF    
Sbjct: 1   IVVKIGGSVVS------DLDKVIDDIANFGERLIVVHGGGNYVNEYLKRLGVEPKFVTSP 54

Query: 85  NGL--RITDQQTAEVVEMVLAGSINKKIVSLINQTGTQAIGICGKDGNMVFAEKARHSLR 142
           +G+  R TD++T EV  MV+ G INKKIV+ ++  G +A+G+ G DG ++ A++ +  +R
Sbjct: 55  SGIRSRYTDKETLEVFVMVM-GLINKKIVARLHSLGVKAVGLTGLDGRLLEAKR-KEIVR 112

Query: 143 LSPNTKK 149
           ++   +K
Sbjct: 113 VNERGRK 119


>gnl|CDD|58607 cd04241, AAK_FomA-like, AAK_FomA-like: This CD includes a
           fosfomycin biosynthetic gene product, FomA, and similar
           proteins found in a wide range of organisms. Together,
           the fomA and fomB genes in the fosfomycin biosynthetic
           gene cluster of Streptomyces wedmorensis confer
           high-level fosfomycin resistance. FomA and FomB proteins
           converted fosfomycin to fosfomycin monophosphate and
           fosfomycin diphosphate in the presence of ATP and a
           magnesium ion, indicating that FomA and FomB catalyzed
           phosphorylations of fosfomycin and fosfomycin
           monophosphate, respectively. FomA and related  sequences
           in this CD are members of the Amino Acid Kinase
           Superfamily (AAK)..
          Length = 252

 Score = 28.7 bits (64), Expect = 0.75
 Identities = 23/108 (21%), Positives = 40/108 (37%), Gaps = 19/108 (17%)

Query: 27  TIVVKYGGHVMNCTDLSKDFVNDI------ALLKKSNITPVIVHGGG----PQIGAVLEK 76
            I++K GG V+   D  +    +        L +  +   V+VHGGG    P+       
Sbjct: 1   MIILKLGGSVITDKDRPETIREENLERIARELAEAIDEKLVLVHGGGSFGHPKAKEYGLP 60

Query: 77  MGIKSKFENGLRITDQQTAEVVEMVLAGSINKKIVSLINQTGTQAIGI 124
            G  S    G+  T +   E+         N  +V  + + G  A+ +
Sbjct: 61  DGDGSFSAEGVAETHEAMLEL---------NSIVVDALLEAGVPAVSV 99


>gnl|CDD|58601 cd04235, AAK_CK, AAK_CK: Carbamate kinase (CK) catalyzes both the
          ATP-phosphorylation of carbamate and carbamoyl
          phosphate (CP) utilization with the production of ATP
          from ADP and CP. Both CK (this CD) and nonhomologous CP
          synthetase synthesize carbamoyl phosphate, an essential
          precursor of arginine and pyrimidine bases, in the
          presence of ATP, bicarbonate, and ammonia. CK is a
          homodimer of 33 kDa subunits and is a member of the
          Amino Acid Kinase Superfamily (AAK)..
          Length = 308

 Score = 28.5 bits (64), Expect = 0.77
 Identities = 12/28 (42%), Positives = 17/28 (60%)

Query: 50 IALLKKSNITPVIVHGGGPQIGAVLEKM 77
          +A L K+    VI HG GPQ+G +L + 
Sbjct: 34 LADLIKNGHEVVITHGNGPQVGNLLLQN 61


>gnl|CDD|30895 COG0549, ArcC, Carbamate kinase [Amino acid transport and
          metabolism].
          Length = 312

 Score = 28.3 bits (63), Expect = 0.85
 Identities = 13/36 (36%), Positives = 17/36 (47%)

Query: 50 IALLKKSNITPVIVHGGGPQIGAVLEKMGIKSKFEN 85
          IA L  S    VI HG GPQ+G +L +       + 
Sbjct: 35 IADLIASGYEVVITHGNGPQVGLLLLQNEAADSEKG 70


>gnl|CDD|48440 cd01911, proteasome_alpha, proteasome alpha subunit. The 20S
           proteasome, multisubunit proteolytic complex, is the
           central enzyme of nonlysosomal protein degradation in
           both the cytosol and nucleus. It is composed of 28
           subunits arranged as four homoheptameric rings that
           stack on top of one another forming an elongated
           alpha-beta-beta-alpha cylinder with a central cavity.
           The proteasome alpha and beta subunits are members of
           the N-terminal nucleophile (Ntn)-hydrolase superfamily.
           Their N-terminal threonine residues are exposed as a
           nucleophile in peptide bond hydrolysis. Mammals have 7
           different alpha and 10 different beta proteasome subunit
           genes while archaea have one of each..
          Length = 209

 Score = 28.1 bits (63), Expect = 1.0
 Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 1/34 (2%)

Query: 114 INQTGTQAIGICGKDGNMVFAEKARHSLRLSPNT 147
           +    T A+GI GKDG ++  EK   S  L P++
Sbjct: 24  VKNGST-AVGIKGKDGVVLAVEKKVTSKLLDPSS 56


>gnl|CDD|48449 cd03751, proteasome_alpha_type_3, proteasome_alpha_type_3. The 20S
           proteasome, multisubunit proteolytic complex, is the
           central enzyme of nonlysosomal protein degradation in
           both the cytosol and nucleus. It is composed of 28
           subunits arranged as four homoheptameric rings that
           stack on top of one another forming an elongated
           alpha-beta-beta-alpha cylinder with a central cavity.
           The proteasome alpha and beta subunits are members of
           the N-terminal nucleophile (Ntn)-hydrolase superfamily.
           Their N-terminal threonine residues are exposed as a
           nucleophile in peptide bond hydrolysis. Mammals have 7
           alpha and 7 beta proteasome subunits while archaea have
           one of each..
          Length = 212

 Score = 27.5 bits (61), Expect = 1.4
 Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 1/36 (2%)

Query: 114 INQTGTQAIGICGKDGNMVFAEKARHSLRLSPNTKK 149
           +  +GT AIGI  KDG ++  EK   S    P + K
Sbjct: 27  VENSGT-AIGIRCKDGVVLAVEKLVTSKLYEPGSNK 61


>gnl|CDD|145673 pfam02637, GatB_Yqey, GatB domain.  This domain is found in GatB.
           It is about 140 amino acid residues long. This domain is
           found at the C terminus of GatB, which transamidates
           Glu-tRNA to Gln-tRNA.
          Length = 148

 Score = 26.8 bits (60), Expect = 2.4
 Identities = 7/25 (28%), Positives = 16/25 (64%)

Query: 87  LRITDQQTAEVVEMVLAGSINKKIV 111
             +T +  AE+++++  G+I+ KI 
Sbjct: 38  SPLTPEHLAELIKLIDEGTISGKIA 62


>gnl|CDD|133132 cd06601, GH31_lyase_GLase, GLases (alpha-1,4-glucan lyases) are
          glycosyl hydrolase family 31 (GH31) enzymes that
          degrade alpha-1,4-glucans and maltooligosaccharides via
          a nonhydrolytic pathway to yield 1,5-D-anhydrofructose
          from the nonreducing end. GLases cleave the bond
          between C1 and O1 of the nonreducing sugar residue of
          alpha-glucans to generate a monosaccharide product with
          a double bond between C1 and C2. This family
          corresponds to subgroup 2 in the Ernst et al
          classification of GH31 enzymes.
          Length = 332

 Score = 26.3 bits (58), Expect = 3.2
 Identities = 11/23 (47%), Positives = 16/23 (69%)

Query: 45 DFVNDIALLKKSNITPVIVHGGG 67
          D +++  L   +NITPVI +GGG
Sbjct: 71 DNLHNKGLKCSTNITPVISYGGG 93


>gnl|CDD|48452 cd03754, proteasome_alpha_type_6, proteasome_alpha_type_6. The 20S
           proteasome, multisubunit proteolytic complex, is the
           central enzyme of nonlysosomal protein degradation in
           both the cytosol and nucleus. It is composed of 28
           subunits arranged as four homoheptameric rings that
           stack on top of one another forming an elongated
           alpha-beta-beta-alpha cylinder with a central cavity.
           The proteasome alpha and beta subunits are members of
           the N-terminal nucleophile (Ntn)-hydrolase superfamily.
           Their N-terminal threonine residues are exposed as a
           nucleophile in peptide bond hydrolysis. Mammals have 7
           alpha and 7 beta proteasome subunits while archaea have
           one of each..
          Length = 215

 Score = 26.3 bits (58), Expect = 3.4
 Identities = 8/34 (23%), Positives = 16/34 (47%)

Query: 114 INQTGTQAIGICGKDGNMVFAEKARHSLRLSPNT 147
           +   G  ++ + GKD  +V  +K      + P+T
Sbjct: 25  VKNAGLTSVAVRGKDCAVVVTQKKVPDKLIDPST 58


>gnl|CDD|109795 pfam00752, XPG_N, XPG N-terminal domain. 
          Length = 100

 Score = 25.4 bits (56), Expect = 6.7
 Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 1/38 (2%)

Query: 31 KYGGHVMNCTDLSKDFVNDIALLKKSNITPVIVHGGGP 68
          + G  + N T     F + +  LK   I P+ V  GGP
Sbjct: 46 QLGNALQN-TSHLMGFFSRLCRLKDFGIKPIFVFDGGP 82


>gnl|CDD|29131 cd02056, alpha-1-antitrypsin_like, alpha-1-antitrypsin_like. This
           family contains a variety of different members of clade
           A of the serpin superfamily. They include the classical
           serine proteinase inhibitors, alpha-1-antitrypsin and
           alpha-1-antichymotrypsin, protein C inhibitor,
           kallistatin, and noninhibitory serpins, like
           corticosteroid and thyroxin binding globulins. In
           general, SERine Proteinase INhibitors (serpins) exhibit
           conformational polymorphism shifting from native to
           cleaved, latent, delta, or polymorphic forms. Many
           serpins, such as antitrypsin and antichymotrypsin,
           function as serine protease inhibitors which regulate
           blood coagulation cascades. Non-inhibitory serpins
           perform many diverse functions such as chaperoning
           proteins or transporting hormones. Serpins are of
           medical interest because mutants have been associated
           with blood clotting disorders, emphysema, cirrhosis, and
           dementia..
          Length = 361

 Score = 25.1 bits (55), Expect = 8.3
 Identities = 17/61 (27%), Positives = 27/61 (44%), Gaps = 9/61 (14%)

Query: 69  QIGAVLEKMGIKSKFENG---LRITDQQTAEVVEMVLAGSINKKIVSLINQTGTQAIGIC 125
            +  +L KMGI   F +      IT+Q   +V + V       K V  +++ GT+A    
Sbjct: 270 NLKDILPKMGITDVFSDKADLSGITEQPNLKVSKAV------HKAVLDVDEKGTEAAAAT 323

Query: 126 G 126
           G
Sbjct: 324 G 324


>gnl|CDD|35405 KOG0184, KOG0184, KOG0184, 20S proteasome, regulatory subunit alpha
           type PSMA3/PRE10 [Posttranslational modification,
           protein turnover, chaperones].
          Length = 254

 Score = 24.9 bits (54), Expect = 8.4
 Identities = 10/34 (29%), Positives = 15/34 (44%)

Query: 116 QTGTQAIGICGKDGNMVFAEKARHSLRLSPNTKK 149
           +     IGI  KDG ++  EK   S    P + +
Sbjct: 32  ENSGTCIGIKCKDGVVLAVEKLITSKLYEPGSNE 65


>gnl|CDD|36679 KOG1466, KOG1466, KOG1466, Translation initiation factor 2B, alpha
           subunit (eIF-2Balpha/GCN3) [Translation, ribosomal
           structure and biogenesis].
          Length = 313

 Score = 24.9 bits (54), Expect = 8.8
 Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 13/75 (17%)

Query: 65  GGGPQIGAVLEKMGIKSKFENGLRITDQQTA---EVVEMVLAGSINKKIVS---LINQTG 118
           G G  +   L+K+GI         + D       E V++VL G+  + +V    +IN+ G
Sbjct: 168 GSGKLMAKELKKLGIPVTL-----VLDSAVGYVMERVDLVLVGA--EGVVESGGIINKIG 220

Query: 119 TQAIGICGKDGNMVF 133
           T  + +C K  N  F
Sbjct: 221 TYQVAVCAKSMNKPF 235


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.317    0.135    0.375 

Gapped
Lambda     K      H
   0.267   0.0801    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,667,861
Number of extensions: 80586
Number of successful extensions: 262
Number of sequences better than 10.0: 1
Number of HSP's gapped: 259
Number of HSP's successfully gapped: 29
Length of query: 150
Length of database: 6,263,737
Length adjustment: 85
Effective length of query: 65
Effective length of database: 4,426,972
Effective search space: 287753180
Effective search space used: 287753180
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.1 bits)